git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38459 bc3139a8-67e5-0310-9ffc-ced21a209358
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@@ -1,7 +1,7 @@ |
1 | 1 |
Package: crlmm |
2 | 2 |
Type: Package |
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Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for SNP 5.0 and 6.0 arrays. |
4 |
-Version: 1.0.68 |
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+Version: 1.0.69 |
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Date: 2008-12-30 |
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Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu> |
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Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu> |
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@@ -953,7 +953,6 @@ biasAdj <- function(plateIndex, envir, priorProb){ |
953 | 953 |
plate <- envir[["plate"]] |
954 | 954 |
if(missing(priorProb)) priorProb <- rep(1/4, 4) ##uniform |
955 | 955 |
emit <- array(NA, dim=c(nrow(A), ncol(A), 10))##SNPs x sample x 'truth' |
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- |
|
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lA <- log2(A) |
958 | 957 |
lB <- log2(B) |
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X <- cbind(lA, lB) |
... | ... |
@@ -995,7 +994,11 @@ biasAdj <- function(plateIndex, envir, priorProb){ |
995 | 994 |
hemDel <- apply(hemDel, c(1,2), sum) |
996 | 995 |
norm <- apply(norm, c(1, 2), sum) |
997 | 996 |
amp <- apply(amp, c(1,2), sum) |
998 |
- |
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+ total <- hemDel + norm + amp |
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+ hemDel <- hemDel/total |
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+ norm <- norm/total |
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+ amp <- amp/total |
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+ envir[["posteriorProb"]] <- list(hemDel=hemDel, norm=norm, amp=amp) |
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999 | 1002 |
tmp <- array(NA, dim=c(nrow(A), ncol(A), 4)) |
1000 | 1003 |
tmp[, , 1] <- homDel |
1001 | 1004 |
tmp[, , 2] <- hemDel |
... | ... |
@@ -6,6 +6,15 @@ |
6 | 6 |
- Allele plots |
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- M v S plots |
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+R. Scharpf (after next release) |
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+ |
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+- crlmm should return a SnpSet object with elements A, B, calls, and |
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+ confs in the assayData when save.it=TRUE. These objects can be very |
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+ big, so... |
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+ |
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+- crlmm function should have an option to return nothing and write to |
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+ file a SnpSet object for each chromosome. This would help the copy |
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+ number part that runs by chromosome |
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9 | 18 |
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10 | 19 |
##################################### |
11 | 20 |
### FOR CNRMA |